Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

tag_button

FMODB ID: L7ZR9

Calculation Name: 5CHX-A-Xray372

Preferred Name: Cardiac myosin

Target Type: PROTEIN COMPLEX

Ligand Name: n-dimethyl-lysine

ligand 3-letter code: MLY

PDB ID: 5CHX

Chain ID: A

ChEMBL ID: CHEMBL3831286

UniProt ID: P12883

Base Structure: X-ray

Registration Date: 2023-09-26

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptAll
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water No
Procedure Auto-FMO protocol ver. 2.20220422
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 212
LigandCharge MLY=1
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1933189.613059
FMO2-HF: Nuclear repulsion 1847178.119081
FMO2-HF: Total energy -86011.493978
FMO2-MP2: Total energy -86260.863107


3D Structure
Snapshot
 
Ligand structure

ligand structure
Ligand Interaction
ligand interaction
Ligand binding energy
"
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
N/AN/AN/AN/AN/AN/A


Interactive mode: IFIE and PIEDA for fragment #1(A:0:SER)


Summations of interaction energy for fragment #1(A:0:SER)
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
-6.941-4.4770.006-1.419-1.050.002
Interaction energy analysis for fragmet #1(A:0:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.030 / q_NPA : -0.016
Distance from base fragment(s) [Å]
Dist
Interaction energy by IFIE and PIEDA
[kcal/mol]
| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >
Fragment charge [e]
FCHARGE q_Mulliken
q_NPA q(I=>J)
Residue
Res #    RES   
Sort
Graph Options
X Axis Label
Y Axis Max Y Axis Min
Display   
frag_NumFragment number. ChainChain species. Res #Residue number. RES3-letter code of amino acid residue, ligand and solvent molecule. FCHARGEFormal charge [e]. q_MullikenFragment charge evaluated by Mulliken charge [e]. q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e]. DISTDistance from Ligand [Å]. TotalIFIE at MP2 level [kcal/mol]. ESElectro static interaction energy by PIEDA [kcal/mol]. EXExchange-repulsion energy by PIEDA [kcal/mol]. CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol]. DI(MP2)Dispersion energy by PIEDA [kcal/mol]. q(I=>J)Charge transfer value from I to J fragmens [e].
3A2GLU-1-0.900-0.9393.453-1.9700.5080.008-1.382-1.1040.002
4A3ARG10.8000.8446.2751.4221.4220.0000.0000.0000.000
5A4MLY10.8580.9599.6800.4480.4480.0000.0000.0000.000
6A5ILE00.0290.01413.182-0.054-0.0540.0000.0000.0000.000
7A6SER0-0.036-0.03615.8940.0490.0490.0000.0000.0000.000
8A7ARG10.9170.96819.3960.1740.1740.0000.0000.0000.000
9A8ILE00.0160.01323.0510.0160.0160.0000.0000.0000.000
10A9HIS00.0150.00625.620-0.008-0.0080.0000.0000.0000.000
11A10LEU00.0050.01827.3330.0020.0020.0000.0000.0000.000
12A11VAL00.013-0.00230.5150.0090.0090.0000.0000.0000.000
13A12SER0-0.031-0.01532.8910.0070.0070.0000.0000.0000.000
14A13GLU-1-0.864-0.94031.935-0.161-0.1610.0000.0000.0000.000
15A14PRO00.0270.01232.980-0.005-0.0050.0000.0000.0000.000
16A15SER0-0.038-0.01333.950-0.001-0.0010.0000.0000.0000.000
17A16ILE0-0.021-0.00229.721-0.001-0.0010.0000.0000.0000.000
18A17THR0-0.050-0.03026.114-0.003-0.0030.0000.0000.0000.000
19A18HIS0-0.025-0.01925.429-0.012-0.0120.0000.0000.0000.000
20A19PHE0-0.023-0.03020.6230.0130.0130.0000.0000.0000.000
21A20LEU00.0190.01219.072-0.002-0.0020.0000.0000.0000.000
22A21GLN00.0110.01513.2040.0140.0140.0000.0000.0000.000
23A22VAL00.0180.00814.1660.0050.0050.0000.0000.0000.000
24A23SER00.0380.0108.8520.0130.0130.0000.0000.0000.000
25A24TRP0-0.062-0.0398.985-0.055-0.0550.0000.0000.0000.000
26A25GLU-1-0.901-0.9414.371-4.093-4.069-0.001-0.0270.0040.000
27A26MLY10.9500.9595.3720.3600.322-0.001-0.0100.0500.000
28A27THR00.0030.0017.7230.0480.0480.0000.0000.0000.000
29A28LEU00.0420.03311.264-0.096-0.0960.0000.0000.0000.000
30A29GLU-1-0.850-0.91213.7520.0150.0150.0000.0000.0000.000
31A30SER0-0.045-0.03611.040-0.011-0.0110.0000.0000.0000.000
32A31GLY00.0300.01713.196-0.041-0.0410.0000.0000.0000.000
33A32PHE0-0.080-0.05311.782-0.047-0.0470.0000.0000.0000.000
34A33VAL00.0200.02311.6440.0700.0700.0000.0000.0000.000
35A34ILE0-0.014-0.01413.701-0.018-0.0180.0000.0000.0000.000
36A35THR00.0250.02016.3340.0270.0270.0000.0000.0000.000
37A36LEU00.0030.02918.4570.0090.0090.0000.0000.0000.000
38A37THR0-0.020-0.03620.635-0.017-0.0170.0000.0000.0000.000
39A38ASP-1-0.771-0.88822.999-0.230-0.2300.0000.0000.0000.000
40A39GLY0-0.014-0.01324.709-0.023-0.0230.0000.0000.0000.000
41A40HIS0-0.049-0.01726.612-0.004-0.0040.0000.0000.0000.000
42A41SER0-0.079-0.05325.6390.0020.0020.0000.0000.0000.000
43A42ALA00.0340.02120.926-0.001-0.0010.0000.0000.0000.000
44A43TRP0-0.009-0.01122.2780.0190.0190.0000.0000.0000.000
45A44THR0-0.003-0.02916.498-0.003-0.0030.0000.0000.0000.000
46A45GLY00.0420.02718.2630.0450.0450.0000.0000.0000.000
47A46THR0-0.052-0.03214.303-0.119-0.1190.0000.0000.0000.000
48A47VAL00.0010.02215.9040.0660.0660.0000.0000.0000.000
49A48SER0-0.032-0.05015.665-0.033-0.0330.0000.0000.0000.000
50A49GLU-1-0.845-0.93715.569-0.011-0.0110.0000.0000.0000.000
51A50SER0-0.056-0.01617.2590.0420.0420.0000.0000.0000.000
52A51GLU-1-0.788-0.86019.742-0.275-0.2750.0000.0000.0000.000
53A52ILE0-0.024-0.00416.7020.0170.0170.0000.0000.0000.000
54A53SER0-0.076-0.06520.5790.0320.0320.0000.0000.0000.000
55A54GLN0-0.065-0.03522.8110.0150.0150.0000.0000.0000.000
56A55GLU-1-0.825-0.91824.299-0.141-0.1410.0000.0000.0000.000
57A56ALA0-0.058-0.03124.3590.0110.0110.0000.0000.0000.000
58A57ASP-1-0.956-0.97426.352-0.028-0.0280.0000.0000.0000.000
59A58ASP-1-0.838-0.90728.915-0.081-0.0810.0000.0000.0000.000
60A59MET0-0.123-0.04828.8390.0000.0000.0000.0000.0000.000
61A60ALA0-0.041-0.01131.1010.0070.0070.0000.0000.0000.000
62A61MET0-0.086-0.03127.2190.0070.0070.0000.0000.0000.000
63A62GLU-1-0.827-0.91225.4780.0310.0310.0000.0000.0000.000
64A63MLY10.9260.94819.030-0.006-0.0060.0000.0000.0000.000
65A64GLY00.0470.03221.336-0.009-0.0090.0000.0000.0000.000
66A65MLY10.8400.89722.111-0.025-0.0250.0000.0000.0000.000
67A66TYR00.001-0.01922.622-0.008-0.0080.0000.0000.0000.000
68A67VAL00.0480.01817.729-0.018-0.0180.0000.0000.0000.000
69A68GLY0-0.004-0.00919.842-0.010-0.0100.0000.0000.0000.000
70A69GLU-1-0.782-0.86721.711-0.057-0.0570.0000.0000.0000.000
71A70LEU00.0270.02519.543-0.016-0.0160.0000.0000.0000.000
72A71ARG10.9110.94912.953-0.103-0.1030.0000.0000.0000.000
73A72MLY10.7970.92318.8600.0110.0110.0000.0000.0000.000
74A73ALA00.0090.00221.978-0.012-0.0120.0000.0000.0000.000
75A74LEU0-0.006-0.00518.843-0.011-0.0110.0000.0000.0000.000
76A75LEU00.0030.01214.410-0.042-0.0420.0000.0000.0000.000
77A76SER0-0.029-0.00917.8480.0040.0040.0000.0000.0000.000
78A77GLY00.0040.02020.1180.0140.0140.0000.0000.0000.000
79A78ALA0-0.045-0.03020.7910.0230.0230.0000.0000.0000.000
80A79GLY0-0.024-0.00324.5940.0070.0070.0000.0000.0000.000
81A80PRO0-0.042-0.00927.1100.0060.0060.0000.0000.0000.000
82A81ALA0-0.034-0.05026.4080.0010.0010.0000.0000.0000.000
83A82ASP-1-0.851-0.91928.431-0.091-0.0910.0000.0000.0000.000
84A83VAL0-0.0010.00228.9840.0000.0000.0000.0000.0000.000
85A84TYR0-0.041-0.05826.3430.0040.0040.0000.0000.0000.000
86A85THR00.0300.03428.828-0.004-0.0040.0000.0000.0000.000
87A86PHE00.0260.00223.939-0.006-0.0060.0000.0000.0000.000
88A87ASN0-0.023-0.00928.5460.0140.0140.0000.0000.0000.000
89A88PHE00.0370.00626.399-0.011-0.0110.0000.0000.0000.000
90A89SER00.0270.03129.9880.0090.0090.0000.0000.0000.000
91A90MLY10.8500.95129.8170.1950.1950.0000.0000.0000.000
92A91GLU-1-0.902-0.96630.963-0.172-0.1720.0000.0000.0000.000
93A92SER0-0.051-0.03532.0150.0010.0010.0000.0000.0000.000
94A93CYS0-0.044-0.00926.555-0.009-0.0090.0000.0000.0000.000
95A94TYR00.0400.02926.671-0.014-0.0140.0000.0000.0000.000
96A95PHE0-0.012-0.01123.7860.0030.0030.0000.0000.0000.000
97A96PHE00.010-0.00526.6710.0010.0010.0000.0000.0000.000
98A97PHE00.0130.00323.2420.0000.0000.0000.0000.0000.000
99A98GLU-1-0.783-0.87927.993-0.099-0.0990.0000.0000.0000.000
100A99MLY10.8180.90928.4120.0480.0480.0000.0000.0000.000
101A100ASN0-0.028-0.03230.6880.0050.0050.0000.0000.0000.000
102A101LEU0-0.028-0.01333.7410.0040.0040.0000.0000.0000.000
103A102MLY10.9040.91936.3660.0260.0260.0000.0000.0000.000
104A103ASP-1-0.902-0.93339.353-0.052-0.0520.0000.0000.0000.000
105A104VAL0-0.018-0.00338.3370.0000.0000.0000.0000.0000.000
106A105SER0-0.021-0.00334.5820.0030.0030.0000.0000.0000.000
107A106PHE0-0.007-0.00930.4880.0060.0060.0000.0000.0000.000
108A107ARG10.8600.93029.7530.1190.1190.0000.0000.0000.000
109A108LEU0-0.037-0.01924.9250.0090.0090.0000.0000.0000.000
110A109GLY00.1050.04525.3650.0010.0010.0000.0000.0000.000
111A110SER0-0.127-0.05225.7830.0030.0030.0000.0000.0000.000
112A111PHE00.0510.02021.189-0.013-0.0130.0000.0000.0000.000
113A112ASN00.0140.00723.4410.0280.0280.0000.0000.0000.000
114A113LEU0-0.058-0.02520.603-0.030-0.0300.0000.0000.0000.000
115A114GLU-1-0.871-0.93621.929-0.319-0.3190.0000.0000.0000.000
116A115MLY10.9000.95222.4640.2110.2110.0000.0000.0000.000
117A116VAL00.0090.02019.2280.0070.0070.0000.0000.0000.000
118A117GLU-1-0.889-0.95222.166-0.346-0.3460.0000.0000.0000.000
119A118ASN0-0.065-0.03818.5360.0210.0210.0000.0000.0000.000
120A119PRO00.0420.02820.979-0.040-0.0400.0000.0000.0000.000
121A120ALA00.011-0.01320.978-0.025-0.0250.0000.0000.0000.000
122A121GLU-1-0.871-0.90417.332-0.457-0.4570.0000.0000.0000.000
123A122VAL00.0430.01815.792-0.055-0.0550.0000.0000.0000.000
124A123ILE0-0.0020.00216.744-0.041-0.0410.0000.0000.0000.000
125A124ARG10.8670.91217.9770.4040.4040.0000.0000.0000.000
126A125GLU-1-0.792-0.85510.699-1.313-1.3130.0000.0000.0000.000
127A126LEU00.0360.02213.759-0.035-0.0350.0000.0000.0000.000
128A127ILE0-0.002-0.00615.2760.0260.0260.0000.0000.0000.000
129A128CYS0-0.057-0.03314.1500.0600.0600.0000.0000.0000.000
130A129TYR00.1160.0597.831-0.033-0.0330.0000.0000.0000.000
131A130CYS0-0.067-0.02612.6760.0690.0690.0000.0000.0000.000
132A131LEU0-0.0220.00315.7540.0740.0740.0000.0000.0000.000
133A132ASP-1-0.876-0.93712.121-0.520-0.5200.0000.0000.0000.000
134A133THR0-0.012-0.02412.2460.0750.0750.0000.0000.0000.000
135A134THR0-0.079-0.05213.5340.0960.0960.0000.0000.0000.000
136A135ALA00.0050.00416.0260.0510.0510.0000.0000.0000.000
137A136GLU-1-0.922-0.95910.139-0.155-0.1550.0000.0000.0000.000
138A137ASN0-0.050-0.03514.5220.1110.1110.0000.0000.0000.000
139A138GLN0-0.056-0.01717.0020.0150.0150.0000.0000.0000.000
140A139ALA00.0710.04017.4040.0240.0240.0000.0000.0000.000
141A140MLY10.8690.92312.260-0.012-0.0120.0000.0000.0000.000
142A141ASN00.008-0.00618.4110.0330.0330.0000.0000.0000.000
143A142GLU-1-0.870-0.93521.7100.0070.0070.0000.0000.0000.000
144A143HIS0-0.016-0.00920.481-0.004-0.0040.0000.0000.0000.000
145A1590HIS00.0160.00518.9930.0130.0130.0000.0000.0000.000
146A1591LEU0-0.003-0.00323.6340.0010.0010.0000.0000.0000.000
147A1592ARG10.8980.96421.627-0.074-0.0740.0000.0000.0000.000
148A1593VAL0-0.0100.00123.6970.0040.0040.0000.0000.0000.000
149A1594VAL0-0.017-0.01626.8790.0000.0000.0000.0000.0000.000
150A1595ASP-1-0.904-0.94229.3700.0550.0550.0000.0000.0000.000
151A1596SER00.0520.03029.9490.0000.0000.0000.0000.0000.000
152A1597LEU0-0.039-0.00928.2810.0010.0010.0000.0000.0000.000
153A1598GLN0-0.019-0.01732.306-0.005-0.0050.0000.0000.0000.000
154A1599THR00.0220.00935.000-0.005-0.0050.0000.0000.0000.000
155A1600SER0-0.038-0.03334.2290.0000.0000.0000.0000.0000.000
156A1601LEU0-0.005-0.00534.902-0.002-0.0020.0000.0000.0000.000
157A1602ASP-1-0.824-0.85938.1990.0420.0420.0000.0000.0000.000
158A1603ALA00.0260.01040.010-0.003-0.0030.0000.0000.0000.000
159A1604GLU-1-0.890-0.95339.2660.0720.0720.0000.0000.0000.000
160A1605THR0-0.071-0.03541.946-0.003-0.0030.0000.0000.0000.000
161A1606ARG10.7710.84344.040-0.045-0.0450.0000.0000.0000.000
162A1607SER00.0180.01744.718-0.003-0.0030.0000.0000.0000.000
163A1608ARG10.9180.95743.749-0.053-0.0530.0000.0000.0000.000
164A1609ASN00.0080.00147.4010.0000.0000.0000.0000.0000.000
165A1610GLU-1-0.796-0.86949.8310.0370.0370.0000.0000.0000.000
166A1611ALA00.0060.00450.000-0.001-0.0010.0000.0000.0000.000
167A1612LEU0-0.021-0.01050.486-0.001-0.0010.0000.0000.0000.000
168A1613ARG10.7990.86853.530-0.038-0.0380.0000.0000.0000.000
169A1614VAL0-0.003-0.00354.980-0.002-0.0020.0000.0000.0000.000
170A1615MLY10.8430.90654.686-0.042-0.0420.0000.0000.0000.000
171A1616MLY10.9570.97657.148-0.031-0.0310.0000.0000.0000.000
172A1617MLY10.8390.91159.677-0.034-0.0340.0000.0000.0000.000
173A1618MET00.0050.00557.6860.0000.0000.0000.0000.0000.000
174A1619GLU-1-0.800-0.88358.9800.0390.0390.0000.0000.0000.000
175A1620GLY0-0.014-0.00362.772-0.001-0.0010.0000.0000.0000.000
176A1621ASP-1-0.826-0.91064.0890.0320.0320.0000.0000.0000.000
177A1622LEU0-0.010-0.00164.085-0.001-0.0010.0000.0000.0000.000
178A1623ASN00.0330.01866.781-0.001-0.0010.0000.0000.0000.000
179A1624GLU-1-0.863-0.91868.9330.0240.0240.0000.0000.0000.000
180A1625MET0-0.027-0.01766.940-0.001-0.0010.0000.0000.0000.000
181A1626GLU-1-0.918-0.95368.3540.0310.0310.0000.0000.0000.000
182A1627ILE0-0.035-0.02072.325-0.001-0.0010.0000.0000.0000.000
183A1628GLN0-0.072-0.04774.811-0.001-0.0010.0000.0000.0000.000
184A1629LEU0-0.0020.00673.650-0.001-0.0010.0000.0000.0000.000
185A1630SER0-0.023-0.01076.370-0.001-0.0010.0000.0000.0000.000
186A1631HIS0-0.014-0.01678.161-0.001-0.0010.0000.0000.0000.000
187A1632ALA00.0350.01379.666-0.001-0.0010.0000.0000.0000.000
188A1633ASN00.008-0.00277.685-0.001-0.0010.0000.0000.0000.000
189A1634ARG10.9120.95881.798-0.022-0.0220.0000.0000.0000.000
190A1635MET0-0.0090.00384.400-0.001-0.0010.0000.0000.0000.000
191A1636ALA00.0020.00984.5060.0000.0000.0000.0000.0000.000
192A1637ALA00.005-0.00485.6220.0000.0000.0000.0000.0000.000
193A1638GLU-1-0.808-0.89587.4530.0180.0180.0000.0000.0000.000
194A1639ALA00.0290.02089.795-0.001-0.0010.0000.0000.0000.000
195A1640GLN00.004-0.00488.980-0.001-0.0010.0000.0000.0000.000
196A1641MLY10.8180.90088.482-0.019-0.0190.0000.0000.0000.000
197A1642GLN00.0100.02193.8460.0000.0000.0000.0000.0000.000
198A1643VAL00.0140.00293.8380.0000.0000.0000.0000.0000.000
199A1644MLY10.9600.97994.532-0.018-0.0180.0000.0000.0000.000
200A1645SER0-0.030-0.02797.0530.0000.0000.0000.0000.0000.000
201A1646LEU0-0.003-0.00698.5450.0000.0000.0000.0000.0000.000
202A1647GLN0-0.015-0.01396.0560.0000.0000.0000.0000.0000.000
203A1648SER0-0.079-0.046101.2280.0000.0000.0000.0000.0000.000
204A1649LEU00.0570.027103.4370.0000.0000.0000.0000.0000.000
205A1650LEU0-0.0230.016103.4070.0000.0000.0000.0000.0000.000
206A1651MLY10.9380.969100.293-0.017-0.0170.0000.0000.0000.000
207A1652ASP-1-0.832-0.907106.5670.0150.0150.0000.0000.0000.000
208A1653THR0-0.031-0.013109.0940.0000.0000.0000.0000.0000.000
209A1654GLN0-0.027-0.031106.5020.0000.0000.0000.0000.0000.000
210A1655ILE0-0.038-0.010110.6990.0000.0000.0000.0000.0000.000
211A1656GLN0-0.063-0.032112.7260.0000.0000.0000.0000.0000.000
212A1657LEU0-0.081-0.031113.7880.0000.0000.0000.0000.0000.000